Faces suddenly missing
It is hard to comment without seeing the blend file, however, you can try:


Un-hiding all faces (Alt + H); and/or
The Make Normals Consistent commend. Highlight all faces (using A in face mode), and then access the command by hitting space bar and searching for it.


I would also run the Remove Doubles command, just to make sure you have not created a face on top of another face when trying to "fill in" the gaps.